PDB-4y1n: Oceanobacillus iheyensis group II intron domain 1 with iridium he...

ID or keywords:

Entry

Database: PDB / ID: 4y1n

Title

Oceanobacillus iheyensis group II intron domain 1 with iridium hexamine

Components

group II intron, domain 1

Keywords

rna /

transferase /

group II intron /

domain 1 / iridium hexamine

Function / homology

IRIDIUM HEXAMMINE ION / : / : /

RNA / RNA (> 10) / RNA (> 100)

Function and homology information

Biological species

Oceanobacillus iheyensis HTE831 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 3 Å

Authors

Zhao, C. / Rajashankar, K.R. / Marcia, M. / Pyle, A.M.

Citation

Journal: Nat.Chem.Biol. / Year: 2015
Title: Crystal structure of group II intron domain 1 reveals a template for RNA assembly.
Authors: Zhao, C. / Rajashankar, K.R. / Marcia, M. / Pyle, A.M.

History

Deposition	Feb 8, 2015	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 14, 2015	Provider: repository / Type: Initial release
Revision 1.1	Nov 11, 2015	Group: Database references
Revision 1.2	Dec 2, 2015	Group: Database references
Revision 1.3	Feb 28, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4y1n.cif.gz	572.7 KB	Display	PDBx/mmCIF format
PDB format	pdb4y1n.ent.gz	468.8 KB	Display	PDB format
PDBx/mmJSON format	4y1n.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/y1/4y1n ftp://data.pdbj.org/pub/pdb/validation_reports/y1/4y1n	HTTPS FTP

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Related structure data

Related structure data	4y1oC C: citing same article (ref.)
Similar structure data	4y1o-2 4y1o-1 5l6h-1 22020 5iud-2 7k7y-2 22900 7luf-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#121 - Jan 2010 70S Ribosomes similarity (2) #130 - Oct 2010 Riboswitches similarity (3) #16 - Apr 2001 Aminoacyl-tRNA Synthetases similarity (1) #157 - Jan 2013 Transfer-Messenger RNA similarity (2) #260 - Aug 2021 Ribonuclease P similarity (2) #253 - Jan 2021 Expressome similarity (2) #181 - Jan 2015 Cascade and CRISPR similarity (1) #229 - Jan 2019 Fluorescent RNA Aptamers similarity (1) #146 - Feb 2012 Aminoglycoside Antibiotics similarity (2) #15 - Mar 2001 Transfer RNA similarity (1) #249 - Sep 2020 SARS-CoV-2 RNA-dependent RNA Polymerase similarity (1) #10 - Oct 2000 Ribosome similarity (2) #65 - May 2005 Self-splicing RNA similarity (3) #87 - Mar 2007 Zinc Fingers similarity (1) #210 - Jun 2017 Adenine Riboswitch in Action similarity (1) #245 - May 2020 Spliceosomes similarity (2) #226 - Oct 2018 Aminoglycoside Antibiotics and Resistance similarity (2) #262 - Oct 2021 Fifty Years of Open Access to PDB Structures similarity (2) #98 - Feb 2008 Small Interfering RNA similarity (1) #105 - Sep 2008 Ribonuclease A similarity (1) #161 - May 2013 Ricin similarity (2) #266 - Feb 2022 Oligosaccharyltransferase similarity (2) #227 - Nov 2018 Telomerase similarity (2) #230 - Feb 2019 Initiation Factor eIF4E similarity (1) #143 - Nov 2011 Toll-like Receptors similarity (1) #106 - Oct 2008 Poly(A) Polymerase similarity (1) #81 - Sep 2006 Elongation Factors similarity (1) #104 - Aug 2008 Selenocysteine Synthase similarity (1) #89 - May 2007 Aconitase and Iron Regulatory Protein 1 similarity (1) #241 - Jan 2020 Twenty Years of Molecules similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#121 - Jan 2010
70S Ribosomes
similarity (2)
#130 - Oct 2010
Riboswitches
similarity (3)
#16 - Apr 2001
Aminoacyl-tRNA Synthetases
similarity (1)
#157 - Jan 2013
Transfer-Messenger RNA
similarity (2)
#260 - Aug 2021
Ribonuclease P
similarity (2)
#253 - Jan 2021
Expressome
similarity (2)
#181 - Jan 2015
Cascade and CRISPR
similarity (1)
#229 - Jan 2019
Fluorescent RNA Aptamers
similarity (1)
#146 - Feb 2012
Aminoglycoside Antibiotics
similarity (2)
#15 - Mar 2001
Transfer RNA
similarity (1)
#249 - Sep 2020
SARS-CoV-2 RNA-dependent RNA Polymerase
similarity (1)
#10 - Oct 2000
Ribosome
similarity (2)
#65 - May 2005
Self-splicing RNA
similarity (3)
#87 - Mar 2007
Zinc Fingers
similarity (1)
#210 - Jun 2017
Adenine Riboswitch in Action
similarity (1)
#245 - May 2020
Spliceosomes
similarity (2)
#226 - Oct 2018
Aminoglycoside Antibiotics and Resistance
similarity (2)
#262 - Oct 2021
Fifty Years of Open Access to PDB Structures
similarity (2)
#98 - Feb 2008
Small Interfering RNA
similarity (1)
#105 - Sep 2008
Ribonuclease A
similarity (1)
#161 - May 2013
Ricin
similarity (2)
#266 - Feb 2022
Oligosaccharyltransferase
similarity (2)
#227 - Nov 2018
Telomerase
similarity (2)
#230 - Feb 2019
Initiation Factor eIF4E
similarity (1)
#143 - Nov 2011
Toll-like Receptors
similarity (1)
#106 - Oct 2008
Poly(A) Polymerase
similarity (1)
#81 - Sep 2006
Elongation Factors
similarity (1)
#104 - Aug 2008
Selenocysteine Synthase
similarity (1)
#89 - May 2007
Aconitase and Iron Regulatory Protein 1
similarity (1)
#241 - Jan 2020
Twenty Years of Molecules
similarity (1)

Deposited unit

A: group II intron, domain 1

B: group II intron, domain 1

hetero molecules

187 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: group II intron, domain 1

hetero molecules

defined by author&software
93.1 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: group II intron, domain 1

hetero molecules

defined by author&software
93.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	83.738, 131.200, 84.640
Angle α, β, γ (deg.)	90.00, 91.71, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: RNA chain	group II intron, domain 1 / Mass: 89198.922 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Oceanobacillus iheyensis HTE831 (bacteria) / References: GenBank: 42632302
#2: Chemical	... ChemComp-IRI / IRIDIUM HEXAMMINE ION Mass: 294.400 Da / Num. of mol.: 28 / Source method: obtained synthetically / Formula: H₁₈IrN₆
#3: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#4: Chemical	ChemComp-K / POTASSIUM ION Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 2.62 Å³/Da / Density % sol: 52.97 %
Crystal grow	Temperature: 298.15 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 80 mM NaCl, 24 mM KCl, 5 mM MgCl2, 40 mM NaCacodylate, 18% MPD, 8 mM spermine-4HCl

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.105 Å
Detector	Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 14, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.105 Å / Relative weight: 1
Reflection	Resolution: 3→44.44 Å / Num. obs: 71447 / % possible obs: 99.08 % / Redundancy: 6.8 % / B_iso Wilson estimate: 84.6 Å² / Net I/σ(I): 17.68
Reflection shell	Resolution: 3→3.1 Å / Redundancy: 6.8 % / Mean I/σ(I) obs: 1.77 / % possible all: 98.77

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Processing

Software

Name	Version	Classification
PHENIX	(phenix.refine: 1.9_1678)	refinement
XDS	January 10, 2014	data reduction
XDS	January 10, 2014	data scaling
SHELXDE	2013/2	phasing
PHENIX	(phenix.autosol: 1.9_1678)	phasing

Refinement

Method to determine structure:

SAD / Resolution: 3→44.438 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 0.44 / Phase error: 27.71 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2458	3578	5.01 %
R_work	0.1828	-	-
obs	0.1861	71447	99.17 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 3→44.438 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	0	10910	205	1	11116

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	12384
X-RAY DIFFRACTION	f_angle_d	1.339	19446
X-RAY DIFFRACTION	f_dihedral_angle_d	15.28	6060
X-RAY DIFFRACTION	f_chiral_restr	0.056	2540
X-RAY DIFFRACTION	f_plane_restr	0.008	508

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
3.0001-3.0395	0.428	134	0.3716	2567	X-RAY DIFFRACTION	99
3.0395-3.0812	0.3959	135	0.3301	2637	X-RAY DIFFRACTION	99
3.0812-3.1252	0.3505	114	0.2798	2673	X-RAY DIFFRACTION	99
3.1252-3.1718	0.3374	135	0.2584	2530	X-RAY DIFFRACTION	98
3.1718-3.2214	0.3192	124	0.2335	2604	X-RAY DIFFRACTION	99
3.2214-3.2742	0.3029	143	0.226	2629	X-RAY DIFFRACTION	100
3.2742-3.3306	0.2964	151	0.2201	2581	X-RAY DIFFRACTION	100
3.3306-3.3911	0.2842	124	0.2146	2680	X-RAY DIFFRACTION	100
3.3911-3.4563	0.307	116	0.1973	2673	X-RAY DIFFRACTION	99
3.4563-3.5269	0.2568	153	0.1996	2610	X-RAY DIFFRACTION	99
3.5269-3.6035	0.2545	136	0.1876	2561	X-RAY DIFFRACTION	100
3.6035-3.6873	0.2654	169	0.1871	2616	X-RAY DIFFRACTION	99
3.6873-3.7795	0.2517	169	0.1715	2588	X-RAY DIFFRACTION	99
3.7795-3.8816	0.2934	133	0.1833	2588	X-RAY DIFFRACTION	99
3.8816-3.9958	0.2592	149	0.1757	2616	X-RAY DIFFRACTION	99
3.9958-4.1246	0.2437	109	0.1643	2619	X-RAY DIFFRACTION	100
4.1246-4.2719	0.2338	117	0.1594	2614	X-RAY DIFFRACTION	100
4.2719-4.4428	0.2595	137	0.1633	2667	X-RAY DIFFRACTION	100
4.4428-4.6448	0.2217	140	0.1617	2627	X-RAY DIFFRACTION	100
4.6448-4.8894	0.2382	123	0.1538	2622	X-RAY DIFFRACTION	99
4.8894-5.1953	0.2083	152	0.1557	2566	X-RAY DIFFRACTION	98
5.1953-5.5958	0.227	127	0.1444	2630	X-RAY DIFFRACTION	100
5.5958-6.1576	0.2174	128	0.1563	2613	X-RAY DIFFRACTION	99
6.1576-7.0455	0.2016	144	0.1719	2630	X-RAY DIFFRACTION	99
7.0455-8.8651	0.2277	140	0.1888	2573	X-RAY DIFFRACTION	99
8.8651-44.4431	0.2227	176	0.1955	2555	X-RAY DIFFRACTION	98

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	-0.0314	0.1021	-0.1899	0.0952	0.1156	-0.0077	-0.4449	0.0058	-0.0217	0.6599	0.2026	0.4844	0.4334	0.3884	-0.0296	1.1424	0.1203	0.2375	0.6794	0.0276	0.8589	-14.7158	-60.4879	-60.0105
2	1.0913	-0.8272	-0.0278	1.3085	0.6715	0.6957	-0.419	-0.209	0.1768	0.4126	0.4031	-0.1844	0.1668	0.1358	0.0003	0.6757	0.0956	-0.1038	0.6519	0.005	0.5542	-32.2275	-31.9311	-43.2576
3	0.823	0.471	1.0131	0.4746	-0.0033	0.8099	-0.3403	-0.0364	0.5142	-0.1841	0.0912	0.0269	-0.1707	0.1516	-0	0.6006	-0.0209	-0.1346	0.7661	-0.117	0.9275	9.9513	-41.8095	-71.5109
4	0.0477	-0.6069	0.0809	1.246	0.3348	0.6141	0.1607	0.312	-0.1802	-0.2435	-0.185	-0.245	0.3676	0.5101	0.0108	0.4793	-0	0.099	0.7433	0.0116	0.499	-34.3667	-39.2217	-75.3445
5	-0.3593	-0.7066	0.4612	-0.2243	0.507	1.0308	0.0267	0.1394	0.3205	0.049	-0.0977	-0.1649	-0.118	0.3053	0	0.6652	0.006	0.0612	0.7329	0.152	0.7173	-35.9277	-22.3159	-73.0756
6	1.1314	-0.1128	-0.024	-0.692	0.0929	0.0725	-0.1167	0.1939	0.1498	0.1326	-0.0349	-0.0368	-0.1634	0.0609	0.0001	0.701	-0.0416	-0.0194	0.5977	0.1254	0.5807	-41.4073	-25.2338	-68.7905
7	1.1467	-1.0218	0.3696	-0.2184	0.3167	0.6165	-0.7156	-0.2451	-0.3057	0.2992	0.3905	0.3129	0.5692	0.5119	-0.0293	0.8151	-0.0558	0.0924	0.2922	0.0486	0.6943	-12.4996	-58.4475	-63.8515
8	0.4633	-0.5142	-0.4394	0.1354	0.2812	-0.7736	0.2068	-0.3087	-0.242	-0.0613	-0.5182	-0.3162	0.261	0.8136	-0.0074	0.6363	-0.0719	-0.1224	0.8689	-0.0771	0.5184	10.0237	-41.9863	-28.7965
9	-0.6835	-0.8724	0.123	1.6081	0.2626	1.0096	0.3117	0.0558	0.0354	-0.3812	-0.2383	0.3965	0.0693	0.108	-0.0003	0.5784	0.0109	-0.136	0.7219	-0.0552	0.7494	-0.5457	-19.0344	-47.0002
10	-0.7693	0.0142	-0.0946	0.8751	0.3583	-0.1484	0.1548	0.0654	0.2938	0.1543	0.1203	0.4296	-0.0792	-0.2994	0.0005	0.6838	-0.1391	-0.0906	0.7134	0.0983	0.7853	-11.4685	-52.9048	-22.0153
11	-0.1142	0.497	0.5088	-0.0112	0.3068	0.4032	0.0577	-0.0491	-0.3301	0.5113	0.0049	0.0661	0.2275	-0.0254	-0.0003	1.0074	0.1081	0.0127	0.6647	0.0022	0.7266	7.2675	-18.4681	-9.1921
12	0.2217	-0.4474	-0.2532	0.9923	0.4693	-0.0095	-0.039	-0.3077	0.3713	0.5061	-0.0139	-0.3029	0.9142	-0.8545	-0.0352	0.9426	-0.2459	0.3158	0.9615	0.0693	0.5463	-10.5777	-7.4345	-3.7769
13	0.5569	-0.3373	-0.1136	0.4511	1.2064	0.2491	-0.1693	-0.3435	0.1347	0.0926	-0.0515	0.2207	-0.0834	-0.1933	-0.1267	0.6392	-0.0194	0.0535	0.8163	-0.0434	0.8101	-12.6362	-6.0238	-29.2628
14	1.1152	0.2032	0.2234	1.166	0.609	0.3813	-0.0421	-0.407	0.0334	0.0094	-0.3864	0.544	0.3766	-0.1944	-1.0843	0.6666	-0.1469	0.1277	0.8131	-0.2444	0.7956	-19.1588	-1.5742	-11.708
15	0.1982	-0.2667	0.2059	0.4078	0.6692	-0.2104	-0.1148	-0.1238	-0.158	0.2904	0.1852	-0.124	0.6458	0.1297	0.0002	0.7342	0.0077	0.0469	0.5595	-0.0429	0.663	9.9848	-14.4229	-22.4984
16	-0.6273	-0.2837	0.0034	0.1548	0.1505	0.4576	0.1062	0.0205	-0.1371	-0.0266	-0.1206	0.3	0.4559	-0.3146	-0.0001	0.7597	-0.0079	-0.0117	0.8183	-0.0313	0.7003	12.9143	-46.9061	-23.1301

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 6 through 21 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 22 through 76 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 77 through 113 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 114 through 155 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 156 through 186 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 187 through 245 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 246 through 270 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid -3 through 24 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 25 through 78 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 79 through 120 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 121 through 144 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 145 through 160 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 161 through 208 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 209 through 224 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 225 through 246 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 247 through 270 )

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